A couple of things to keep in mind:
The FET switch in the controller is between the motor and battery (-).
Battery (+) goes straight to the motor inside a typical brushed controller. There's also a freewheel diode not shown on your drawing. In this case, it's not real important.
If you're running full throttle with the boost on, and your BMS decides to open, the full voltage of both packs will be on the BMS. It would be the same if the boost pack was ahead of the controller.
At partial throttle, especially during acceleration, the current in the motor wires might be MUCH higher than the current coming out of the battery, which might make the boost pack unhappy.
If possible, the boost pack should probably go next to the main battery.
If the controller voltage rating is not high enough for that, then the way you drew it should work.